#ctat-metagenomics For foreign transcript detection, we leverage Centrifuge and Kraken, leveraging RNA-Seq reads and Trinity-reconstructed transcripts. Our efforts here are being carried out in collaboration with the group of Steven Salzberg at JHU.
Click the 'wiki' link at top for the ctat-metagenomics documentation.
Note, if you're going to clone the code from github, do it recursively like so:
git clone --recursive https://github.com/NCIP/ctat-metagenomics.git